Several publications and patent documents are cited throughout the specification in order to describe the state of the art to which this invention pertains. Each of these citations is incorporated herein by reference as though set forth in full.
Gene activity is controlled by a combination of proximal and distal regulatory elements that can be separated by up to hundreds of kilobases. Longstanding questions have been how these elements interact functionally to regulate gene expression, how gene specificity is achieved, and how unwanted effects on nearby irrelevant genes are avoided. The use of chromosome conformation capture (3C) and its derivatives has revealed that distant chromosomal elements can be juxtaposed to form chromatin loops, thus providing one mechanism of long-range enhancer function (Cullen et al. (1993) Science 261:203-206; Dekker et al. (2002) Science 295:1306-1311). Chromatin looping has been discovered at numerous gene loci, and reflects a widespread organizing principle of the chromatin fiber (Dean, A. (2011) Brief Funct. Genomics 10:3-10; Kadauke et al. (2009) Biochim. Biophys. Acta, 1789:17-25; Miele et al. (2008) Mol. Biosyst., 4:1046-1057; Schoenfelder et al. (2010) Curr. Opin. Genet. Dev., 20:127-133; Sexton et al. (2009) Semin. Cell Dev. Biol., 20:849-855). Although looping can occur at genes prior to their full activation, the onset of transcription is tightly associated with additional looped interactions (Palstra et al. (2003) Nat. Genet., 35:190-194; Spilianakis et al. (2004) Nat. Immunol., 5:1017-1027; Vernimmen et al. (2007) EMBO J., 26:2041-2051). However, based on studies using pharmacological inhibitors of transcription elongation, it has become clear that ongoing transcription is dispensable for sustaining preformed chromatin loops (Mitchell et al. (2008) Genes Dev., 22:20-25; Palstra et al. (2008) PLoS ONE 3:e1661). Moreover, chromatin looping is not limited to active genes. For example, upon repression of the Kit gene, loss of an enhancer-promoter loop is accompanied by de novo loop formation within the gene body (Jing et al. (2008) Mol. Cell., 29:232-242). These studies indicate that chromatin loops are highly dynamic and occur at active and repressed genes but leave open the question as to whether these long-range interactions are a cause or consequence of dynamic changes in transcription initiation.